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root/OpenMD/branches/development/src/visitors/OtherVisitor.cpp

Comparing:
trunk/src/visitors/OtherVisitor.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "selection/SelectionManager.hpp"
43		#include "visitors/OtherVisitor.hpp"
#	Line 223 | Line 224 | namespace OpenMD {
224		return result;
225		}
226
227	<	//----------------------------------------------------------------------------//
227	>	//------------------------------------------------------------------------//
228
229	<	XYZVisitor::XYZVisitor(SimInfo *info) :
230	<	BaseVisitor(), seleMan(info), evaluator(info){
231	<	this->info = info;
232	<	visitorName = "XYZVisitor";
233	<
234	<	evaluator.loadScriptString("select all");
235	<
236	<	if (!evaluator.isDynamic()) {
237	<	seleMan.setSelectionSet(evaluator.evaluate());
238	<	}
239	<	posOnly_ = false;
229	>	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
230	>	evaluator(info), doPositions_(true),
231	>	doVelocities_(false),
232	>	doForces_(false), doVectors_(false),
233	>	doCharges_(false) {
234	>	this->info = info;
235	>	visitorName = "XYZVisitor";
236	>
237	>	evaluator.loadScriptString("select all");
238	>
239	>	if (!evaluator.isDynamic()) {
240	>	seleMan.setSelectionSet(evaluator.evaluate());
241		}
242	<
242	>	}
243	>
244		XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
245	<	BaseVisitor(), seleMan(info), evaluator(info) {
246	<	this->info = info;
247	<	visitorName = "XYZVisitor";
248	<
249	<	evaluator.loadScriptString(script);
250	<
251	<	if (!evaluator.isDynamic()) {
252	<	seleMan.setSelectionSet(evaluator.evaluate());
253	<	}
254	<	posOnly_ = false;
245	>	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
246	>	doVelocities_(false), doForces_(false), doVectors_(false),
247	>	doCharges_(false) {
248	>
249	>	this->info = info;
250	>	visitorName = "XYZVisitor";
251	>
252	>	evaluator.loadScriptString(script);
253	>
254	>	if (!evaluator.isDynamic()) {
255	>	seleMan.setSelectionSet(evaluator.evaluate());
256		}
257	+	}
258
259		void XYZVisitor::visit(Atom *atom) {
260		if (isSelected(atom))
#	Line 260 | Line 265 | namespace OpenMD {
265		if (isSelected(datom))
266		internalVisit(datom);
267		}
268	<
268	>
269		void XYZVisitor::visit(RigidBody *rb) {
270		if (isSelected(rb))
271		internalVisit(rb);
272		}
273	<
273	>
274		void XYZVisitor::update() {
275		//if dynamic, we need to re-evaluate the selection
276		if (evaluator.isDynamic()) {
277		seleMan.setSelectionSet(evaluator.evaluate());
278		}
279		}
280	<
280	>
281		void XYZVisitor::internalVisit(StuntDouble *sd) {
282		GenericData *                     data;
283		AtomData *                        atomData;
284		AtomInfo *                        atomInfo;
285		std::vector<AtomInfo *>::iterator i;
286		char                              buffer[1024];
287	<
287	>
288		//if there is not atom data, just skip it
289		data = sd->getPropertyByName("ATOMDATA");
290	<
290	>
291		if (data != NULL) {
292		atomData = dynamic_cast<AtomData *>(data);
293	<
293	>
294		if (atomData == NULL)
295		return;
296		} else
297		return;
298
299	<	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
300	<	std::string bn = baseTypeName(at);
301	<
302	<	if (posOnly_){
303	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
304	<	atomInfo = atomData->nextAtomInfo(i) ) {
305	<	if (atomInfo->hasCharge) {
306	<	sprintf(buffer,
307	<	"%s%15.8f%15.8f%15.8f%15.8f",
308	<	bn.c_str(),
309	<	atomInfo->pos[0],
310	<	atomInfo->pos[1],
311	<	atomInfo->pos[2],
312	<	atomInfo->charge);
313	<	} else {
309	<	sprintf(buffer,
310	<	"%s%15.8f%15.8f%15.8f",
311	<	bn.c_str(),
312	<	atomInfo->pos[0],
313	<	atomInfo->pos[1],
314	<	atomInfo->pos[2]);
315	<	}
316	<	frame.push_back(buffer);
299	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
300	>	atomInfo = atomData->nextAtomInfo(i) ) {
301	>
302	>	std::string line;
303	>	sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
304	>	line += buffer;
305	>
306	>	if (doPositions_){
307	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
308	>	atomInfo->pos[1], atomInfo->pos[2]);
309	>	line += buffer;
310	>	}
311	>	if (doCharges_ && atomInfo->hasCharge) {
312	>	sprintf(buffer, "%15.8f", atomInfo->charge);
313	>	line += buffer;
314		}
315	<	}else{
316	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
317	<	atomInfo = atomData->nextAtomInfo(i) ) {
318	<	if (atomInfo->hasCharge) {
322	<	sprintf(buffer,
323	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
324	<	bn.c_str(),
325	<	atomInfo->pos[0],
326	<	atomInfo->pos[1],
327	<	atomInfo->pos[2],
328	<	atomInfo->charge,
329	<	atomInfo->dipole[0],
330	<	atomInfo->dipole[1],
331	<	atomInfo->dipole[2]);
332	<	} else {
333	<	sprintf(buffer,
334	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
335	<	bn.c_str(),
336	<	atomInfo->pos[0],
337	<	atomInfo->pos[1],
338	<	atomInfo->pos[2],
339	<	atomInfo->dipole[0],
340	<	atomInfo->dipole[1],
341	<	atomInfo->dipole[2]);
342	<	}
343	<	frame.push_back(buffer);
315	>	if (doVectors_ && atomInfo->hasVector) {
316	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
317	>	atomInfo->vec[1], atomInfo->vec[2]);
318	>	line += buffer;
319		}
320	<	}
320	>	if (doVelocities_ && atomInfo->hasVelocity) {
321	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
322	>	atomInfo->vel[1], atomInfo->vel[2]);
323	>	line += buffer;
324	>	}
325	>	if (doForces_ && atomInfo->hasForce) {
326	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
327	>	atomInfo->frc[1], atomInfo->frc[2]);
328	>	line += buffer;
329	>	}
330	>	frame.push_back(line);
331	>	}
332		}
333
334		bool XYZVisitor::isSelected(StuntDouble *sd) {
#	Line 352 | Line 338 | namespace OpenMD {
338		void XYZVisitor::writeFrame(std::ostream &outStream) {
339		std::vector<std::string>::iterator i;
340		char buffer[1024];
341	<
341	>
342		if (frame.size() == 0)
343		std::cerr << "Current Frame does not contain any atoms" << std::endl;
344	<
344	>
345		//total number of atoms
346		outStream << frame.size() << std::endl;
347	<
347	>
348		//write comment line
349		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
350		Mat3x3d box = currSnapshot->getHmat();
#	Line 369 | Line 355 | namespace OpenMD {
355		box(0, 0), box(0, 1), box(0, 2),
356		box(1, 0), box(1, 1), box(1, 2),
357		box(2, 0), box(2, 1), box(2, 2));
358	<
358	>
359		outStream << buffer << std::endl;
360	<
360	>
361		for( i = frame.begin(); i != frame.end(); ++i )
362		outStream << *i << std::endl;
363		}
364	<
364	>
365		std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
366		return atomTypeName.substr(0, atomTypeName.find('-'));
367		}
368	<
383	<	std::string XYZVisitor::baseTypeName(AtomType* at) {
384	<	std::vector<AtomType*> ayb = at->allYourBase();
385	<	return ayb[ayb.size()-1]->getName();
386	<	}
387	<
368	>
369		const std::string XYZVisitor::toString() {
370		char        buffer[65535];
371		std::string result;
372	<
372	>
373		sprintf(buffer,
374		"------------------------------------------------------------------\n");
375		result += buffer;
376	<
376	>
377		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
378		result += buffer;
379	<
379	>
380		sprintf(buffer,
381		"Visitor Description: assemble the atom data and output xyz file\n");
382		result += buffer;
#	Line 403 | Line 384 | namespace OpenMD {
384		sprintf(buffer,
385		"------------------------------------------------------------------\n");
386		result += buffer;
387	<
387	>
388		return result;
389		}
390	<
390	>
391		//----------------------------------------------------------------------------//
392	<
392	>
393		void PrepareVisitor::internalVisit(Atom *atom) {
394		GenericData *data;
395		AtomData *   atomData;
396	<
396	>
397		//if visited property is  existed, remove it
398		data = atom->getPropertyByName("VISITED");
399	<
399	>
400		if (data != NULL) {
401		atom->removeProperty("VISITED");
402		}
403	<
403	>
404		//remove atomdata
405		data = atom->getPropertyByName("ATOMDATA");
406
#	Line 488 | Line 469 | namespace OpenMD {
469		visitorName = "WaterTypeVisitor";
470		waterTypeList.insert("TIP3P_RB_0");
471		waterTypeList.insert("TIP4P_RB_0");
472	+	waterTypeList.insert("TIP4P-Ew_RB_0");
473		waterTypeList.insert("TIP5P_RB_0");
474	+	waterTypeList.insert("TIP5P-E_RB_0");
475		waterTypeList.insert("SPCE_RB_0");
476	+	waterTypeList.insert("SPC_RB_0");
477		}
478
479		void WaterTypeVisitor::visit(RigidBody *rb) {
#	Line 502 | Line 486 | namespace OpenMD {
486		std::vector<AtomInfo *>::iterator i;
487
488		rbName = rb->getType();
489	<
489	>
490		if (waterTypeList.find(rbName) != waterTypeList.end()) {
491		myAtoms = rb->getAtoms();
492
493		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
494		++atomIter ) {
495		data = (*atomIter)->getPropertyByName("ATOMDATA");
496	<
496	>
497		if (data != NULL) {
498		atomData = dynamic_cast<AtomData *>(data);
499	<
499	>
500		if (atomData == NULL)
501		continue;
502		} else
503		continue;
504	<
504	>
505		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
506		atomInfo = atomData->nextAtomInfo(i) ) {
507		atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);

Comparing:
trunk/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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